RepeatMasker

RepeatMasker is a tool for identifying repetitive sequence by aligning a library of known repeats to the genome. Recently it has been released as open source software, and is available from repeatmasker.org. In addition, you will also be required to download RepeatMasker Libraries from Repbase once you have registered.

Several speedups have been implemented to allow the tool to use other alignment programs like WU-BLAST instead of Phil Green's cross_match.